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Version: 26.2

Co-Scientist

When deploying Co-Scientist, installing or authenticating the Seqera CLI, using the Co-Scientist panel, or working with projects, you might encounter the following issues.

Deployment​

Check deployment health​

Run the /doctor skill from the Co-Scientist panel or a CLI session. It tests the agent's tools, MCP and Platform connectivity, and code execution, and reports PASS, FAIL, or SKIP per subsystem with remediation steps.

For a non-interactive check, enable SERVICE_INFO_ENABLED on the agent backend and query https://<agent-backend-domain>/v1/service-info. Add ?deep=1 with a Platform access token as a bearer token to run live inference and sandbox checks. See Run deployment diagnostics.

Co-Scientist does not appear in the navigation bar​

The Co-Scientist panel appears only when all of the following are true:

  1. TOWER_AGENT_BACKEND_URL is set on the Platform backend. The Platform Helm chart sets it when the agent-backend subchart is enabled.
  2. You are in an organization workspace. The panel is not available in personal workspaces.
  3. Your organization is included in TOWER_AI_CHAT_ALLOWED_ORGANIZATIONS, or the variable is unset.
  4. Your workspace role includes the chat:execute permission. The View role and custom roles do not include it unless an administrator adds it. See Custom roles.

The Co-Scientist panel opens but requests fail to authenticate​

The panel authenticates to the agent backend with the Platform session cookie. Check that the agent backend domain is a subdomain of a domain shared with Platform. Also check that TOWER_AUTH_COOKIE_DOMAIN is set to that parent domain with a leading dot, for example .platform.example.com. The Platform Helm chart sets it when the agent-backend subchart is enabled.

Approval prompts time out​

The agent backend waits 15 minutes for a local command result. If you leave an approval prompt open longer than that, the request times out. Send your request again and respond to the prompt within 15 minutes.

A session can no longer be resumed​

The agent backend deletes CLI sessions after 14 days and Co-Scientist panel conversations after 180 days. Start a new session. Administrators can change the retention periods. See Sessions.

Installation​

seqera: command not found​

If you see seqera: command not found after installation:

  1. Verify the Seqera CLI installation location:

    which seqera

  2. Ensure the npm global bin directory is on your PATH. Find it with npm config get prefix or npm bin -g:

    # Check the npm global bin directory
    npm bin -g

    # Restart your terminal or run
    source ~/.bashrc  # or ~/.zshrc

npm permission errors​

If you encounter permission errors during installation:

  1. Use the npm prefix option to install to a user-writable directory:

    npm install -g seqera --prefix ~/.npm-global

  2. Add the directory to your PATH:

    export PATH="$HOME/.npm-global/bin:$PATH"

EACCES permission errors on global install​

Avoid running sudo npm install. Either fix npm permissions or install Node through a version manager such as nvm.

Authentication​

Browser doesn't open​

If the browser doesn't open automatically:

  1. Check the terminal output for a URL.
  2. Copy and paste the URL into your browser.
  3. Complete authentication in the browser.

Login timeout​

If authentication times out:

  1. Check that your Seqera Platform URL is reachable from your machine.
  2. Confirm that SEQERA_AUTH_DOMAIN, or authDomain in ~/.config/seqera-ai/config.json, points at your Enterprise deployment, for example https://platform.example.com/api. Run seqera info to see the values the CLI resolved.
  3. If you are on a remote host, set SEQERA_BROWSER_AUTO_OPEN=false. Open the printed URL in a browser on a machine that can reach the callback port (53682 by default, set with SEQERA_AUTH_REDIRECT_PORT).
  4. Log out and log in again.

Token storage errors​

If you see errors related to credential storage:

  1. Check that you have write permissions to ~/.config/seqera-ai/:

    ls -la ~/.config/seqera-ai/

  2. If the directory doesn't exist, create it:

    mkdir -p ~/.config/seqera-ai

Session expired​

If your session has expired, log out and log in again:

seqera logout
seqera login

Projects​

The Projects view does not appear​

The Projects view appears only when all of the following are true:

  1. You are in an organization workspace. Projects are not available in personal workspaces.
  2. TOWER_SCIENTIST_VIEW_ALLOWED_WORKSPACES is unset or empty, or lists the workspace ID. Projects are enabled in every organization workspace by default. See Enable projects.
  3. Your workspace role includes the project_view:read permission. Every predefined role includes it. Custom roles do not unless an organization owner adds it from the Projects permission category. Existing custom roles do not gain it on upgrade. See Permissions.

Existing project_* labels do not appear as projects​

Seqera Platform recognizes only labels with the proj_ prefix. Rename project_* labels to proj_* in workspace settings.

Dataset uploads do not auto-attach the project label​

When you upload a dataset into a project, Seqera Platform does not automatically attach the project's proj_* label.

This issue occurs when a resource carries a proj_* label that was not created in workspace settings. That label has no Platform-assigned ID, and auto-attach requires that ID.

To avoid this issue, create proj_* labels in workspace settings, or with Add project, before applying them to resources. See Projects.

The Projects page shows Get started with projects​

This issue occurs when the workspace has no proj_* labels.

To resolve, select Add project, or ask a workspace admin to create the first proj_* label for the workspace. Creating a project requires permission to create labels. See Create a project.

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